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tristan-f-r
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For the web folder, is that something that can be a separate pull request? It mentions in the high level that this is something that someone can't review right now.
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True! Ill have to make some light changes, but I'll make that separate 👍
ntalluri
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ntalluri
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I did a light review of the PR; did not look to hard at the code itself yet. I mostly was gathering ideas on what was happening from the READMEs.
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Can we change the name of this. DMMM isn't a very universal term to all the algorithms in this config. Maybe something like prize-active?
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Not a big fan of either names, though I'm much more worried for the config being universal to the provided datasets rather than to the provided algorithms.
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Based on how we are setting up the configs for the paper, we will need to make and have each config dataset collection specific instead of algorithm type specific anyways. This would be a better way to organize these configs. Also so people have access to the configs we used.
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the EGFR dataset is also not specific to algorithms that fit into the DMMM category only.
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| edge_files: ["processed/interactome.tsv"] | ||
| node_files: ["processed/prizes.txt"] | ||
| other_files: [] | ||
| - label: dmmmegfr_irefindex |
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| - label: dmmmegfr_irefindex | |
| - label: egfr_irefindex |
Co-authored-by: Neha Talluri <78840540+ntalluri@users.noreply.github.com>
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| When a file is requested, `cached`, `pinned`, and `unpinned` are all downloaded, and we characterize them as follows: |
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Still don't understand what these terms actual are mean and are associated to before them leading to failure or updating; the following descriptions don't help since they involve using multiple terms.
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| ## Snakemake | ||
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| We also provide a `Snakefile`, which can be imported in dataset Snakefiles through: |
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| We also provide a `Snakefile`, which can be imported in dataset Snakefiles through: | |
| We also provide a `Snakefile`, which can contains dataset fetching functions that are imported in dataset specific Snakefiles through: |
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We bundle EGFR along with the rest of the caching infrastructure. Notes:
cache/README.md.pra.yamlfor now, as the only PRAs are the synthetic data and the ResponseNet data, and soon the DepMap data.CONTRIBUTING.mdfile is not finalized, and is simply there to not break Changes to CONTRIBUTING guide #57. I may split all contributing material into Changes to CONTRIBUTING guide #57 later.directory.pycontains unnecessary files from other datasets that were deemed universal.webfolder even though I'm aware no one is currently in a position to review it.